I took a STD test Feb 9th, 2013 and all negative to include both HSV-1/HSV-2IGG. I have had a 3 partners since. 4 weeks after my last sexual encounter, I had some painful sores on the shaft of my penis. They felt like some kind of trauma/friction/rubbing...A few water/clear blisters formed in some areas of the "new" skin, I thought maybe I had rubbed my penis on my zipper or while lifting weights and these new blisters from daily vigorous exercise that I do. Nevertheless, I went to get tested again a few days ago (approx. 5 weeks out from last encounter) and my results were HSV-1 NEG and HSV-2 abnormal 1.22. I have read online that I should definitely have a retest done because of a low positive. I have read that I should seek a Western Blot test if possible. My question is what type (urologist, dermatoligist, etc) of doctor should I go to that would have the best knowledge of HSV-2 and testing for it?

Your lesions seem to be due to HSV 2 only. You need not repeat the test. Clinical presentaion is enough and more important to arrive at the diagnosis. Some other tissue smear examinations also is available to confirm the diagnosis. It can be done in a good clinical pathology laboratory.

Urologist is not the suitable surgeon to consult for your problem. A Dermato-venereologist or an infectious diseases specialist are the ideal persons to be consulted.
Wish you a speedy recovery.
Dr.S.Murugan